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Yorodumi- PDB-4qg4: Crystal structure of the tetrameric GTP/dATP/ATP-bound SAMHD1 (H2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qg4 | ||||||
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Title | Crystal structure of the tetrameric GTP/dATP/ATP-bound SAMHD1 (H210A) mutant catalytic core | ||||||
Components | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | ||||||
Keywords | HYDROLASE / deoxynucleoside triphosphate triphosphohydrolase / 2'-deoxyadenosine-5'-triphosphate / guanosine-5'-triphosphate / HIV restriction factor / dNTPase | ||||||
Function / homology | Function and homology information Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / deoxyribonucleotide catabolic process / dGTP catabolic process ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / deoxyribonucleotide catabolic process / dGTP catabolic process / DNA strand resection involved in replication fork processing / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / site of double-strand break / single-stranded DNA binding / protein homotetramerization / defense response to virus / nucleic acid binding / immune response / innate immune response / DNA damage response / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Koharudin, L.M.I. / Wu, Y. / DeLucia, M. / Mehrens, J. / Gronenborn, A.M. / Ahn, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structural Basis of Allosteric Activation of Sterile alpha Motif and Histidine-Aspartate Domain-containing Protein 1 (SAMHD1) by Nucleoside Triphosphates. Authors: Koharudin, L.M. / Wu, Y. / DeLucia, M. / Mehrens, J. / Gronenborn, A.M. / Ahn, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qg4.cif.gz | 428.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qg4.ent.gz | 348.9 KB | Display | PDB format |
PDBx/mmJSON format | 4qg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qg4_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 4qg4_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 4qg4_validation.xml.gz | 77.1 KB | Display | |
Data in CIF | 4qg4_validation.cif.gz | 104.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/4qg4 ftp://data.pdbj.org/pub/pdb/validation_reports/qg/4qg4 | HTTPS FTP |
-Related structure data
Related structure data | 4qfxC 4qfyC 4qfzC 4qg0C 4qg1C 4qg2C 4bzbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 63341.250 Da / Num. of mol.: 4 / Fragment: UNP residues 113-626 / Mutation: H210A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SAMHD1, MOP5 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases |
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-Non-polymers , 5 types, 585 molecules
#2: Chemical | ChemComp-GTP / #3: Chemical | ChemComp-DTP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M SPG, pH 6.5, 25% PEG1500, 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2013 |
Radiation | Monochromator: Rosenbaum-Rock double-crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→41.743 Å / Num. all: 133665 / Num. obs: 133587 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.79 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 4.79 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BZB Resolution: 2.1→41.743 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 32.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→41.743 Å
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Refine LS restraints |
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LS refinement shell |
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